5-127869728-C-T

Variant names:

• chr5-127869728-C-T
• rs245181
• NM_001317938.2:c.412-5810C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001317938.2(CCDC192):​c.412-5810C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,168 control chromosomes in the GnomAD database, including 42,206 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.74 (42206 hom., cov: 33)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 1 publications found

Genes affected

CCDC192 (HGNC:49566): (coiled-coil domain containing 192)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001317938.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC192	NM_001317938.2	MANE Select	c.412-5810C>T		intron	N/A	NP_001304867.2	A0A9S7N7Z0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC192	ENST00000514853.5	TSL:5 MANE Select	c.412-5810C>T		intron	N/A	ENSP00000490579.2	A0A9S7N7Z0
	CCDC192	ENST00000706942.1		c.469-5810C>T		intron	N/A	ENSP00000516662.1	P0DO97

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112351 AN: 152050 Hom.: 42154 Cov.: 33

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.714

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.739 AC: 112465 AN: 152168 Hom.: 42206 Cov.: 33 AF XY: 0.735 AC XY: 54661 AN XY: 74370

African (AFR) AF: 0.878 AC: 36478 AN: 41542

American (AMR) AF: 0.694 AC: 10612 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2307 AN: 3468

East Asian (EAS) AF: 0.589 AC: 3051 AN: 5178

South Asian (SAS) AF: 0.550 AC: 2651 AN: 4816

European-Finnish (FIN) AF: 0.699 AC: 7382 AN: 10566

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47522 AN: 67992

Other (OTH) AF: 0.713 AC: 1505 AN: 2110

Alfa AF: 0.730 Hom.: 5078

Bravo AF: 0.743

Asia WGS AF: 0.575 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.78
DANN	Benign	0.28
PhyloP100		-0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs245181; hg19: chr5-127205420;